Can you take a screen shot of the folder listing in the Mail left panel on each machine? See if some are listed in a different location in the hierarchy. Post them here if you wish and we can take a look.
Here's how they're set up on the 2 computers. I know there are differences, but what should I do about it?
I believe this is what was pointed out in the TidBITS article "my notes" is not the same as "My notes".
I would suggest first arranging all the folders in the same order on both computers If you do have an iCloud account, you can upload/store your rules there (iCloud Documents & Data) and at least have the same ones be applied with both computers.
That's exactly what I suspect most of all, that since the folders are arranged a bit differently, iCloud is forcing the issue. Hadn't noticed the difference in "My Notes" vs "my notes."
I still find iCloud confusing--especially knowing which computer is the dominant one.
Thanks for your thoughts, I'll play with it & see what happens...